WBConfCall 2013.07.18-Agenda and Minutes

From WormBaseWiki
Revision as of 19:04, 18 July 2013 by Jchan (talk | contribs) (→‎AmiGO2)
Jump to navigationJump to search


Models If anyone wants to discuss anything, but nothing from Me (Paul D.)

Progress on Ontology Browsing


- given a goid, generate an svg graph with clickable nodes and make a separate html table of children if there's too many.
- code is ~120 lines of perl
- using GraphViz to generate an SVG with clickable links to other nodes in the graph.
- using JSON to parse the json from berkeleybop
- using LWP::Simple to get json from berkeleybop
- currently limiting graph to 5 children, and suppressing GOIDs
- arrows in graph follow colours used by amigo

Upcoming Build

Post-IWM Discussion

  • WormMine
    • Can anyone make templates public?
    • If not, should WB curators still be using the staff account to edit or publish templates?


  • It would be helpful, for coordinating helpdesk responses, if we could assign issues to specific people.
    • Either ourselves if we've picked up an issue to answer or...
    • Someone else, which the helpdesk officer could do as part of their duties.
    • I think this would help eliminate redundant efforts and/or responses and allow people to check to see if an issue is already claimed by someone before they start working on a reply.
    • We have a list of people and their responsibilities, but perhaps a more granular list for internal helpdesk purposes would be useful:

Outstanding Helpdesk Issues

Since we didn't have a call on the 4th, I checked over the last month's worth of helpdesk issues.

Here are the issues that are still open, a brief summary, and anyone who's commented. Please check and close an issue if you can.

Also, issues that we haven't responded to at all are in bold.

  • 1437 - still working on it- ky xEs12400 Vancouver large-scale strains and trangenes - Karen, Wen
  • 1438 - RNASeq data access errors in GBrowse- needs help from GBrowse Dev, WebTeam or Hinxton?-ky Died links - Karen
  • 1443 - BLAST with WS235 - Joachim, Chris
  • 1462 - BLAST with suum - Kevin, Abby, Joachim
  • 1466 - Multiple sequence alignments
  • 1471 - Mary Ann proposed a solution through non-git e-mails (now pasted into git). Requires further discussion with curation group-ky n765 is lin-15AB - Karen
  • 1484 - Download table from Interaction widget - Chris
  • 1487 - Genome Browser images larger than 1024 pixels
  • 1488 - had been moved to Helped-ky New widget on Process page - Karen
  • 1500 - Genes in region of genetic map - Raymond
  • 1511 - still working on it-ky Moving bacterial strain genotype - Karen, Mary Ann
  • 1512 - Download list of Other_names - Wen, Chris, JD
  • 1514 - Follow selected genes automatically via email
  • 1517 - GBrowse exports out of frame
  • 1518 - Follow up to 1517, only minus strand
  • 1519 - Orthologs in WormMine - JD, Todd, Michael P.
  • 1531 - Inline chat - Todd, Abby
  • 1541 - Multiword string search Paper class - Michael P., Xiaodong, Karen, Kimberly, Abby
  • 1556 - Widget placement and size - Kimberly, Abby
  • 1557 - WormMine - unrecognized genes in list - Raymond, Chris
  • 1563 - sp11 Downloads - Kimberly, Chris
  • 1564 - BLAST/BLAT - Paul D., Joachim, Kimberly
  • 1572 - Query Contains widget - Mary Ann, Todd,
  • 1582 - Oliver - Submitting consecutive questions


Upcoming Builds

  • WS240
    • Will upload at the end of September and stay on two-month schedule for the time being
    • Think about milestones for WS240 and start a github ticket to collect them
    • Caltech is discussing a new, more process-focused approach to literature curation
    • Will update group on what/how they decide to do this and if there's any coordination that should happen between sites as a result
  • Panagrellus genome
    • Michael P. waiting on Panagrellus submission to Genbank so we can incorporate this genome into WB


  • JD currently on vacation; will need to confirm a few things with him when he gets back:
    • Who can make things public (still staff account only)
    • How often are things made public? Only with each new WormMine release?
    • How often do existing lists, for example, need to be upgraded?

Helpdesk SOP

  • Github may not be the perfect system for what we're trying to do, but it seems to have enough useful features to continue to use it
  • Perhaps we can work on our existing SOP (http://wiki.wormbase.org/index.php/Github_Helpdesk_Working_Document) to help reduce redundancy in efforts and responses to users
  • Some ideas:
    • Everyone on helpdesk rotation should have a github account
    • All issues should be logged in github
    • If an incoming helpdesk issue is not automatically assigned an issue number in github, then the helpdesk officer, or person who answers that email, should add it to github
    • If we can, assign issues to people, including ourselves, to indicate that someone is either working on, or is the point person for, responding to an issue
    • If you've been assigned an issue and don't feel you can respond, you can re-assign it to someone else
    • Users probably don't usually follow the github ticket, so make sure you reply to them via email
    • Try to remember to cc everyone on a reply, so we all know what's been done about an issue
  • If other sites have additional trackers they use, would be nice to have that all consolidated in github

Outstanding Helpdesk Issues

  • Please look over the list again to see if you can close any issues
  • Michael P. will respond to sp11 emails
    • There seems to be two issues, one of missing protein sequences and the other with incorrect URLs